The vertebrate immune system includes adaptive and innate components. The adaptive immune system utilizes effector cells (e.g., B cells and T cells) that express adaptable membrane bound or secreted receptor proteins (e.g., T cell receptors, or B cell receptors or antibodies). For example, T cells can recognize various tumor cells, viruses, or pathogenic organisms through a T cell receptor (TCR). The mammalian immune system can contain αβ and γδ TCRs. An αβ TCR is a heterodimer of an α chain from the TCRA locus and a β chain from the TCRB locus. A γδ TCR is a heterodimer of a γ chain from the TCRG locus and a δ chain from the TCRD locus. These heterodimeric immune recognition receptors recognize epitope peptides presented by the major histocompatibility complex (MHC) class I and II proteins on the surface of antigen-presenting cells (APCs). Binding of TCR to an antigenic epitope peptide on the APC is a central event in T cell activation. This T cell activation can select for T cells that express TCRs with productive binding specificities against tumor or pathogenic antigens.
Each TCR heterodimer contains variable complementarity determining regions (CDRs), as well as framework regions (FRs) and constant regions. The sequence diversity of αβ T cells is largely determined by the amino acid sequence of the complementarity-determining region (CDR) loops of the α and β chain variable domains (CDR1α, CDR2α, CDR3α, CDR1β, CDR2β, and CDR3β). The existence of multiple such gene segments in the TCR α and β chain loci allows for a large number of distinct CDR sequences to be encoded. The diversity of CDR3 α and β is further increased by recombination between variable (V), diversity (D), and joining (J) gene segments in the β chain locus and recombination between V and J gene segments in the α chain locus. CDR3 sequence diversity is also further increased by independent addition and deletion of nucleotides at the Vβ-Dβ, Dβ-Jβ, and Vα-Jα junctions during the process of TCR gene recombination.
Similarly, B cells express adaptive immune receptor immunoglobulins (Igs). These immunoglobulins are known as B cell receptors (BCR) when in their membrane bound form and as antibodies when secreted. These immunoglobulins, consist of two heavy chains (H) from the IGH locus and two light chains (L) from either the IGK (κ) or the IGL (λ) locus, forming an H2L2 structure. The H and L chains each contain complementarity determining regions (CDR) involved in antigen recognition, and a constant domain. The diversity of naïve Igs within an individual is, in part, determined by the sequence of the hypervariable complementarity determining regions (CDRs). Similar to the TCR, the CDR3 domain of IGH chains is created by the combinatorial joining of the VH, DH, and JH gene segments. Hypervariable domain sequence diversity is further increased by independent addition and deletion of nucleotides at the VH-DH, DH-JH, and VH-JH junctions during the process of Ig gene rearrangement. Ig sequence diversity is further augmented by somatic hypermutation (SHM) throughout the rearranged IG gene after a B cell is activated by antigen recognition. The process of SHM can introduce changes in the germline sequence in framework regions, CDR1 and CDR2, as well as in the somatically rearranged CDR3. Binding of a BCR to an antigenic epitope leads to B cell activation. This B cell activation can select for B cells that express BCRs (and antibodies) with productive binding specificities against tumor or pathogenic antigens.
The resident diversity of CDR, framework, diversity, and joining regions of T cell and B cell receptors combined with diversity enhancing recombination and/or somatic hypermutation results in a vast immune repertoire of antigen binding specificities. Identification of such sequences, and the epitopes to which they specifically bind can be useful, e.g., for (1) guiding the design of recombinant T or B cells for immunotherapy against tumor cells, viruses, or pathogenic organisms; (2) identifying novel antibodies for antibody mediated therapy or development of improved diagnostics; (3) monitoring immune system function and/or disease progression; or (4) detection or quantification of tumor cell or pathogenic organism burden in a host subject.